Metallo-toeholds: controlling DNA strand displacement driven by Hg(II) ions.

Toehold-mediated strand displacement is a powerful tool that permits programmable control over DNA hybridization. Here, we developed a mechanism for strand displacement driven by Hg(2+) ions, in which the insertion of thymine-thymine mismatched base pairs on the toeholds provides additional control through variation of the concentration of Hg(2+) ions.

[1]  Erik Winfree,et al.  Dynamic allosteric control of noncovalent DNA catalysis reactions. , 2008, Journal of the American Chemical Society.

[2]  Z. Deng,et al.  Colorimetric Hg2+ detection with a label-free and fully DNA-structured sensor assembly incorporating G-quadruplex halves. , 2009, The Analyst.

[3]  E. Stulz,et al.  A DNA based five-state switch with programmed reversibility. , 2012, Chemical communications.

[4]  Jian-hui Jiang,et al.  Label‐Free Electrochemical Biosensor of Mercury Ions Based on DNA Strand Displacement by Thymine–Hg(II)–Thymine Complex , 2010 .

[5]  S. Wada,et al.  Incorporation of thymine nucleotides by DNA polymerases through T-Hg(II)-T base pairing. , 2010, Angewandte Chemie.

[6]  Lulu Qian,et al.  Supporting Online Material Materials and Methods Figs. S1 to S6 Tables S1 to S4 References and Notes Scaling up Digital Circuit Computation with Dna Strand Displacement Cascades , 2022 .

[7]  G. Seelig,et al.  DNA as a universal substrate for chemical kinetics , 2010, Proceedings of the National Academy of Sciences.

[8]  Jehoshua Bruck,et al.  Neural network computation with DNA strand displacement cascades , 2011, Nature.

[9]  Yi Lu,et al.  Metal ion sensors based on DNAzymes and related DNA molecules. , 2011, Annual review of analytical chemistry.

[10]  Itamar Willner,et al.  DNA machines: bipedal walker and stepper. , 2011, Nano letters.

[11]  A. Turberfield,et al.  A DNA-fuelled molecular machine made of DNA , 2022 .

[12]  Kemin Wang,et al.  Engineering a unimolecular multifunctional DNA probe for analysis of Hg2+ and Ag+ , 2012 .

[13]  Harry M. T. Choi,et al.  Programming biomolecular self-assembly pathways , 2008, Nature.

[14]  N. Seeman,et al.  A robust DNA mechanical device controlled by hybridization topology , 2002, Nature.

[15]  P. Rothemund Folding DNA to create nanoscale shapes and patterns , 2006, Nature.

[16]  Luca Cardelli,et al.  Abstractions for DNA circuit design , 2011, Journal of The Royal Society Interface.

[17]  Chengde Mao,et al.  Molecular gears: a pair of DNA circles continuously rolls against each other. , 2004, Journal of the American Chemical Society.

[18]  D. Y. Zhang,et al.  Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA , 2007, Science.

[19]  Faisal A. Aldaye,et al.  Assembling Materials with DNA as the Guide , 2008, Science.

[20]  Yi Lu,et al.  Small-molecule diagnostics based on functional DNA nanotechnology: a dipstick test for mercury. , 2011, Faraday discussions.

[21]  Metal‐Ion‐Mediated Base Pairs in Nucleic Acids , 2008 .

[22]  A. Ono,et al.  Highly selective oligonucleotide-based sensor for mercury(II) in aqueous solutions. , 2004, Angewandte Chemie.

[23]  D. Y. Zhang,et al.  Control of DNA strand displacement kinetics using toehold exchange. , 2009, Journal of the American Chemical Society.

[24]  J. Piccirilli,et al.  Identification of catalytic metal ion ligands in ribozymes. , 2009, Methods.

[25]  Cheulhee Jung,et al.  "Illusionary" polymerase activity triggered by metal ions: use for molecular logic-gate operations. , 2010, Angewandte Chemie.

[26]  S. Balasubramanian,et al.  A reversible pH-driven DNA nanoswitch array. , 2006, Journal of the American Chemical Society.

[27]  T. Carell,et al.  DNA--metal base pairs. , 2007, Angewandte Chemie.

[28]  Jing Li,et al.  DNAzyme-based colorimetric sensing of lead (Pb2+) using unmodified gold nanoparticle probes , 2008, Nanotechnology.

[29]  Erik Winfree,et al.  Robustness and modularity properties of a non-covalent DNA catalytic reaction , 2010, Nucleic acids research.

[30]  D. Shangguan,et al.  Specific mercury(II) adsorption by thymine-based sorbent. , 2009, Talanta.

[31]  D. Draper,et al.  RNA folding: thermodynamic and molecular descriptions of the roles of ions. , 2008, Biophysical journal.

[32]  A. Ono,et al.  Hg(II) ion specifically binds with T:T mismatched base pair in duplex DNA. , 2010, Chemistry.

[33]  Takashi Fujimoto,et al.  MercuryII-mediated formation of thymine-HgII-thymine base pairs in DNA duplexes. , 2006, Journal of the American Chemical Society.

[34]  Haojun Liang,et al.  Synchronized assembly of gold nanoparticles driven by a dynamic DNA-fueled molecular machine. , 2012, Journal of the American Chemical Society.

[35]  A. Ono,et al.  Binding of metal ions by pyrimidine base pairs in DNA duplexes. , 2011, Chemical Society reviews.

[36]  A. Ono,et al.  Positive cooperativity of the specific binding between Hg2+ ion and T:T mismatched base pairs in duplex DNA , 2012 .

[37]  I. Willner,et al.  Multiplexed analysis of Hg2+ and Ag+ ions by nucleic acid functionalized CdSe/ZnS quantum dots and their use for logic gate operations. , 2009, Angewandte Chemie.

[38]  Xi Chen,et al.  Probing spatial organization of DNA strands using enzyme-free hairpin assembly circuits. , 2012, Journal of the American Chemical Society.

[39]  Jonathan Bath,et al.  Remote toehold: a mechanism for flexible control of DNA hybridization kinetics. , 2011, Journal of the American Chemical Society.

[40]  S. Wada,et al.  Pyrimidine-pyrimidine base pairs stabilized by silver(I) ions. , 2011, Chemical communications.

[41]  Yi Lu,et al.  Highly sensitive "turn-on" fluorescent sensor for Hg2+ in aqueous solution based on structure-switching DNA. , 2008, Chemical communications.

[42]  Haojun Liang,et al.  Real-time study of a DNA strand displacement reaction using dual polarization interferometry. , 2013, Biosensors & bioelectronics.

[43]  Fan Yang,et al.  Dual polarisation interferometry for real-time, label-free detection of interaction of mercury(II) with mercury-specific oligonucleotides. , 2012, Chemical communications.